Re: [Jmol-developers] 2D/3D

Angel,
sorry to confuse, CHIME was able to display a flat version of a 2D file where all z coords were 0.0
There was an extra piece of code in the commercial version that allowed some energy minimisations
and movement of atoms around and then to re-minimise. Its been a while since I played with it.
SCULPT...Automatic molecule conversion from 2D to 3D when pasting from 2D drawing programs
that support the MDL Mol format
Re SMILES, note that the JME generates a different SMILES string to say ChemAxon.
For many years we have had a 1st year tutorial where we provide them with formulae and tell
the students to draw the structures and these are graded by comparing the known SMILES
with what JME calculates.
We had a second version using the ChemZxon programmes and had to redo all the SMILES
strings since they were not the same.
The quizzes were for simple alkyls, more complicated alkyls and aryls and substituted species
with chiral centres etc. The web pages are behind our campus firewall so not publicly accessible
and it is now being maintained by a colleague in the Organic Chem section. Works like a charm...
Robert
Prof. Robert J. Lancashire mailto:robert.lancashire@...
Department of Chemistry Tel (876) 512 3026
University of the West Indies, Kingston 7 Fax (876) 977 1835
Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html
________________________________________
Message: 1
Date: Thu, 29 Apr 2010 12:03:32 +0200
From: Angel Herr?ez <angel.herraez@...>
Subject: Re: [Jmol-developers] 2D/3D project
To: <jmol-developers@...>
Message-ID: <4BD95974.31731.5C2E53@...>
Content-Type: text/plain; charset="US-ASCII"
A few comments:
1. JCP has the advantage of accepting SMILES; which I think is more
widespread and feature-loaded than JME. I also allows more variety
when drawing structures. I have set quizzes that use SMILES to match
user-drawn structures against correct answers. I doubt that JME
string would be capable of not too simple structures.
(I may be wrong in my appreciation of JME capabilities)
2. I think that MOL is a better choice for inter-app transfer than
JME
3. Re. JME specification: some hints at
http://wiki.jmol.org/index.php/File_formats/Coordinates#JME
------------------------------
Message: 2
Date: Thu, 29 Apr 2010 12:05:31 +0200
From: Angel Herr?ez <angel.herraez@...>
Subject: Re: [Jmol-developers] Jmol-developers Digest, Vol 47, Issue 6
To: <jmol-developers@...>
Message-ID: <4BD959EB.19828.5DFDA5@...>
Content-Type: text/plain; charset="ISO-8859-1"
Robert, do you mean that Chime would do 3D starting from a flat
structure? I've never seen that
El 28 Apr 2010 a las 17:34, LANCASHIRE,Robert J escribi?:
> this would then mean Jmol really does provide a replacement for MDL CHIME.....
> Would Jmol then read mol files where all the z coords were zero and be able
> to generate a reasonable representation?

Thread view

Angel,
sorry to confuse, CHIME was able to display a flat version of a 2D file where all z coords were 0.0
There was an extra piece of code in the commercial version that allowed some energy minimisations
and movement of atoms around and then to re-minimise. Its been a while since I played with it.
SCULPT...Automatic molecule conversion from 2D to 3D when pasting from 2D drawing programs
that support the MDL Mol format
Re SMILES, note that the JME generates a different SMILES string to say ChemAxon.
For many years we have had a 1st year tutorial where we provide them with formulae and tell
the students to draw the structures and these are graded by comparing the known SMILES
with what JME calculates.
We had a second version using the ChemZxon programmes and had to redo all the SMILES
strings since they were not the same.
The quizzes were for simple alkyls, more complicated alkyls and aryls and substituted species
with chiral centres etc. The web pages are behind our campus firewall so not publicly accessible
and it is now being maintained by a colleague in the Organic Chem section. Works like a charm...
Robert
Prof. Robert J. Lancashire mailto:robert.lancashire@...
Department of Chemistry Tel (876) 512 3026
University of the West Indies, Kingston 7 Fax (876) 977 1835
Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html
________________________________________
Message: 1
Date: Thu, 29 Apr 2010 12:03:32 +0200
From: Angel Herr?ez <angel.herraez@...>
Subject: Re: [Jmol-developers] 2D/3D project
To: <jmol-developers@...>
Message-ID: <4BD95974.31731.5C2E53@...>
Content-Type: text/plain; charset="US-ASCII"
A few comments:
1. JCP has the advantage of accepting SMILES; which I think is more
widespread and feature-loaded than JME. I also allows more variety
when drawing structures. I have set quizzes that use SMILES to match
user-drawn structures against correct answers. I doubt that JME
string would be capable of not too simple structures.
(I may be wrong in my appreciation of JME capabilities)
2. I think that MOL is a better choice for inter-app transfer than
JME
3. Re. JME specification: some hints at
http://wiki.jmol.org/index.php/File_formats/Coordinates#JME
------------------------------
Message: 2
Date: Thu, 29 Apr 2010 12:05:31 +0200
From: Angel Herr?ez <angel.herraez@...>
Subject: Re: [Jmol-developers] Jmol-developers Digest, Vol 47, Issue 6
To: <jmol-developers@...>
Message-ID: <4BD959EB.19828.5DFDA5@...>
Content-Type: text/plain; charset="ISO-8859-1"
Robert, do you mean that Chime would do 3D starting from a flat
structure? I've never seen that
El 28 Apr 2010 a las 17:34, LANCASHIRE,Robert J escribi?:
> this would then mean Jmol really does provide a replacement for MDL CHIME.....
> Would Jmol then read mol files where all the z coords were zero and be able
> to generate a reasonable representation?

On Thu, Apr 29, 2010 at 6:00 PM, LANCASHIRE,Robert J <
robert.lancashire@...> wrote:
>
> 3. Re. JME specification: some hints at
> http://wiki.jmol.org/index.php/File_formats/Coordinates#JME
>
>
I note that the description on the WIKI should be changed:
from:
The JME Molecular Editor <http://www.molinspiration.com/jme/&gt; (by Peter
Ertl) is an applet which allows to draw, edit and display molecules and
reactions within a web page. Among its output formats there is a proprietary
JME format <http://www.molinspiration.com/jme/doc/jme_functions.html&gt;,
formed by a single line of text with atom and bond data. Jmol has a basic
support to read this format from a file (only single and multipart
structures are supported, but not reactions). Of course, being a drawing
program, the structures produced are flat.
*This support is rather experimental and not much needed, since JME-ME can
also export to 2D MOL format, much better supported by Jmol.*
To:
The JME Molecular Editor <http://www.molinspiration.com/jme/&gt; (by Peter
Ertl) is an applet which allows to draw, edit and display molecules and
reactions within a web page. Among its output formats there is a proprietary
JME format <http://www.molinspiration.com/jme/doc/jme_functions.html&gt;,
formed by a single line of text with atom and bond data. Jmol has a basic
support to read this format from a file (only single structures are
supported, not multipart structures or reactions). Jmol 12.0 will
automatically apply a 2D->3D conversion algorithm to the model. This works
most successfully if stereochemistry is indicated.
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

LANCASHIRE,Robert J wrote:
> sorry to confuse, CHIME was able to display a flat version of a 2D file where all z coords were 0.0
Right, that's what Jmol has always done.
> There was an extra piece of code in the commercial version that allowed some energy minimisations
> and movement of atoms around and then to re-minimise. Its been a while since I played with it.
Oh yes, sculpt. I never used it. Anyway, not in the freeware Chime I
think. No matter, it was just curiosiity.
Yes, my experience with SMILES (and it is often discussed in the web)
is that it is not unique. Even from the same program you get
different siles strings depending on how you draw the structure.
Tricky to solve when you want to do automatic assessment.
My comment was along the line that, given that smiles is non unique,
I doubted that JME could be.
Now I have realized that they are really compeletly different
languages. JME format stores 2D coordinates and bonds, while SMILES
defines chemistry, not coordinates.
So it all will come to see what can JME format do with complex
molecules. On the other hand, Jmol does not (yet?) read SMILES, which
JChemPaint does. But we have MOL which is more of a common standard
for all. Of course, more complex than single-line JME, that's why Bob
and Otis have found such a usefulness for it.
Another thing that popped in my mind: what distance units does JME
use? I've had issues in the past with JCP exporting MOL with very
long bonds because it worked in pixels, not angstroms. This has been
fixed in recent versions of JCP, per my request.

I've made some interesting observations, with flat MOL file models that have the (newly
supported by Jmol) stereo bond codes (1 for up, 6 for down):
(All atoms have z=0)
2 programs that have a good support for the MOLfile standard:
ChemSketch opens the files and depicts them flat with the proper wedge bonds.
Accelrys' Discovery Studio Visualizer 2.0 opens the files and depicts them 3D, so it has done
an optimization behind the scenes, like Jmol does with the
load myFile.mol filter "2D"
method. So this is not unique to Jmol!
However, in the dimethylcyclopentane I just used for testing, DSV retains the proper stereo,
and does not add hydrogens, while Jmol adds H but looses the stereo config when
minimizing.
Now an idea:
The MOL format spec says that flat models should have a 2D tag*. Up to now, Jmol is not
parsing it.
My suggestion: check if the 2D tag is present and, in that case, apply the 3D conversion even
if a plain "load" command is used. That would match in the 2D-MOL files the behaviour with
JME files.
How does it sound?
*) line 2, columns 21-22 should be either "2D" or "3D"

Jmol won't preserve those bond types. It will simply use them transiently to
start the 2D->3D process. Jmol will always convert the JME up and down bond
types to single bonds.
2010/4/30 Angel Herráez <angel.herraez@...>
> Bob, can you check if the info at
> http://wiki.jmol.org/index.php/Support_for_stereochemistry
> is correct and precise?
>
> Thanks
>
>
>
> ------------------------------------------------------------------------------
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@...
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900